The present invention relates generally to handling, measurement, and cleavage of objects at the molecular size scale, that is, with handling, measurement, and cleavage of objects with characteristic dimensions on the order of nanometers.
The art of manipulating individual atoms, molecules, and supramolecular particles is called xe2x80x9cnanomanipulationxe2x80x9d, and is in a very crude state in the year 2001.
The art of nanomanipulation was first proposed by Richard Feynman on Dec. 29, 1959, at the annual meeting of the American Physical Society in a speech titled xe2x80x9cThere""s Plenty of Room at the Bottomxe2x80x9d, in which he noted that
xe2x80x9cThe principles of physics, as far as I can see, do not speak against the possibility of maneuvering things atom by atom. It is not an attempt to violate any laws; it is something, in principle, that can be done; but in practice, it has not been done because we are too big.xe2x80x9d
Feynman, the winner of the 1965 Nobel Prize in physics, further noted in his 1959 speech that xe2x80x9cThe problems of chemistry and biology can be greatly helped if our ability to see what we are doing, and to do things on an atomic level, is ultimately developedxe2x80x94a development which I think cannot be avoided.xe2x80x9d
However, progress in nanomanipulation has been slow.
The scanning tunneling microscope (STM) was developed in 1980; see U.S. Pat. No. 4,343,993. The STM provides, in essence, a means of shoving around atoms and molecules on a slab with a pointy stick. It also provides a crude sense of touch. The atomic force microscope (AFM) was developed subsequently and provides another means of shoving atoms and molecules on a slab with a pointy stick, and also provides a crude sense of feel. Other proximal probe microscopy (PPM) techniques were developed subsequently; all consist of a pointy stick whose tip position is controlled and monitored, and which can report on the profile and properties of a surface over which the stick is dragged. The usual means of controlling the stick""s tip position is a three-axis piezoelectric driver, and the usual means of sensing the tip position is a combination of sensing the voltages applied to the piezoelectric driver and sensing some other quantity such as tunneling current, piezoresistive change, or optical reflection occurring as close as possible to the tip. Scanning probe techniques have been combined with electron microscopy to provide additional sensing means; see, for example xe2x80x9cThree-dimensional manipulation of carbon nanotubes under a scanning electron microscopexe2x80x9d, by MinFeng Yu et al, Nanotechnology, Vol. 10, no. 3, pp. 244-252 (September 1999).
More recently, naturally occurring pores in cell membranes have been used to characterize long-chain molecules; see, for example, U.S. Pat. No. 5,795,782. These pores have fixed dimensions on the order of nanometers. Subsequently, artificially-produced nanopores of fixed dimensions have been developed for the same purpose. Both types of pores have been used to sense the passage of individual long-chain molecules such as DNA molecules, and have provided some information on the structure of such molecules. The xe2x80x9choly grailxe2x80x9d of these techniques, not yet achieved, has been to sense the structure of a molecule passing through a pore to a level as fine as the individual bases in a DNA strand.
The usual means of sensing the passage of a molecule through the pore is to monitor ionic current through a solution filling the pore when a voltage is applied. Reduction in a maximum current implies that the pore is partly blocked by the cross-sectional area of a molecule. Charged molecules float freely in solution, and at random times are pulled through the pore by an electric field existing in the solution. One problem with these techniques is that the passage of an individual molecule through a pore cannot be precisely predicted or controlled; it is a random, stochastic event, and when a molecule enters the pore, it zips through quickly.
Thus, there still exists a need for other means of manipulating and sensing atoms and molecules, and other entities larger than molecules.
The present invention forms an adjustable nanopore, nanotome, or nanotweezer by placing two substrates in close contact such that they form a small adjustable aperture through which a continuous path extends. A first substrate has a first edge situated at a first surface of the first substrate, the first edge having a first region of sharp curvature in the plane of the first surface. A second substrate has a second edge situated at a second surface of the second substrate. The first surface is placed in close contact with the second substrate such that the first edge and the second edge combine to form an arched aperture, the first edge forming the arch, the first region of sharp curvature forming the crown of the arch, the second edge forming the base of the arch, and the two closest approach points of the first and second edges forming the springing points of the arch. The second edge may be straight, or may be curved either convexly toward or concavely away from the first edge. The second edge can be moved with respect to the first edge, using an adjustable movement mechanism, to vary the height of the arch, the area of the arch, and the shape of the arch. The width of the aperture is defined as the diameter of the largest sphere which can pass through the aperture, and this width can be one hundred nanometers and less. The arched aperture can be usefully employed in characterizing, sorting, sieving, cleaving, and holding nanometer-scale substances including molecules, molecular complexes, and supramolecular complexes, and mixtures thereof.
In accordance with several embodiments of the present invention, two monolithic substrates are provided, each having a through-hole, with the first through-hole in the first substrate intersecting a first surface at a first edge, the first edge having a corner region of sharp curvature in the plane of the first surface with a radius of curvature on the order of 3 nanometers, the first through-hole and the first edge being preferably formed by orientation-dependent etching. The second through-hole in the second substrate intersects a second surface at a second edge, and the second hole and second edge are also preferably formed by orientation dependent etching. The first surface is placed in contact with the second surface such that the first edge and second edge combine to form an arched aperture of substantially triangular cross section, the corner region in the first edge forming the crown of the arch or the apex of the triangle. A mechanism is provided to move one substrate relative to the other so as to adjust the size and shape of the aperture.
In one embodiment (nanopore), the first edge and the second edge combine to create a pore of adjustable area and substantially triangular cross section through which a molecule can pass, so as to provide information about the molecule or to separate molecules of different dimensions, such as separating straight-chain hydrocarbons from branched hydrocarbons.
In a second embodiment (nanotome), the first edge and the second edge combine to create a pore of adjustable area and substantially triangular cross section around a stretched long-chain molecule. The area of the pore is then reduced to create a shearing action so as to cut the molecule at a desired point.
In a third embodiment (nanotweezer), the first edge and the second edge combine to create a pore of adjustable area and substantially triangular cross section around a stretched long-chain molecule. The area of the pore is then reduced to capture the molecule at a desired point without cutting it.
In the three embodiments discussed above, the arched aperture is substantially triangular (symmetrical or asymmetrical), and the height of the triangle is altered by moving one element relative to the other, e.g., moving the second edge (base) closer to or further away from the corner (crown or apex) in the first edge.
Alternatively, a second corner region of sharp curvature in the second edge may be formed, and the corner region in the first edge may be combined with the corner region in the second edge to form an arched aperture which is substantially square, more generally substantially rectangular, or more generally substantially rhomboid, in which the area of the rhombus is altered by moving one corner relative to the other corner.
The above embodiments rely on the combined use of corners and edges which can be built with atomically precise dimensions, or with dimensions which are nearly atomically precise, and which can be juxtaposed with long-chain molecular preparations to manipulate such preparations and to provide information on the properties of such preparations.
More generally, the present invention relies on the combined use of a first substrate having a first surface intersected by a first edge having a region of sharp curvature in the plane of the first surface, and a second substrate having a second surface intersected by a second edge, the two edges being juxtaposed with molecular preparations to manipulate such preparations and to provide information on the properties of such preparations. The molecular preparations can include molecules, molecular complexes, ands supramolecular complexes.
In one embodiment, the nanopore of the present invention comprises two monolithic substrates, each containing a through-hole created by orientation-dependent etching. The two substrates are placed in contact with one another in such a manner that the through-holes are placed adjacent to one another, so that a continuous passage through both substrates exists. Further, the two substrates are rotationally adjusted with respect to one another using a goniometer so that a sharp corner of one through-hole is adjacent a sharp edge of the other through-hole, thus creating a nanopore of triangular cross-section. The cross-sectional area of the triangular nanopore is adjusted by moving the corner with respect to the edge using one or more piezoelectric positioners. The shape of the triangular nanopore is adjusted by rotating the corner with respect to the edge using a goniometer.
Specifically, in accordance with a further aspect of the present invention, a method for fabricating the nanopore is provided, which comprises:
providing a first substrate having a flat first major surface;
forming a first edge lying in the plane of the first major surface, the edge having a first region of sharp curvature in the plane of first surface;
providing a second substrate having a flat major second surface;
forming a second edge laying in the plane of the second surface,
placing the first surface in contact with the second surface in such a fashion that the second edge and the first region of sharp curvature form an aperture; and
providing adjustment means to control the width of the aperture.
An ionic solution filling the nanopore has an electrical conductance through the pore which is proportional to the cross-sectional area of the pore. As the cross-sectional area of the pore is adjustably reduced and approaches zero, the ionic conductance through the pore is reduced and approaches zero, and the curve of conductance versus position changes slope when the pore cross-sectional area is reduced to zero. The change in slope, rather than a complete reduction to zero current, occurs because leakage current occurs along the interface between the two substrates, which interface has some roughness allowing some penetration of the ionic solution.
Long-chain polymer molecules which pass through the adjustable nanopore when no adjustment of pore area is being performed interfere with the flow of ionic current, and so the ionic current at constant cross-sectional area may be measured to monitor the passage of such long-chain polymers or to otherwise characterize and/or handle such molecules.
Thus, in accordance with another aspect of the present invention, a method of at least one of characterizing and handling at least one substance selected from the group consisting of molecules, molecular complexes, and supramolecular complexes and mixtures thereof is provided, comprising:
providing a nanopore having a width, the nanopore including a mechanism for adjusting the width of the nanopore;
placing the nanopore in an ionic solution containing at least one copy of the substance to be characterized so that a continuous path of the ionic solution through the nanopore is established;
adjusting the width of the nanopore to a desired first width;
establishing an ionic electric current of desired direction and magnitude through the nanopore; and
sensing at least one of the entrance into the nanopore of the substance to be characterized and the blockage by the nanopore of the path of the substance to be characterized, the sensing occurring by means of a change in the magnitude of the ionic current.
If it is desired to cleave a long molecule, the area of the adjustable nanopore may be changed while electrical current monitoring indicates that the molecule is passing through the nanopore. In this event, the apparatus of the present invention exerts a scissoring action in the molecule, acting to cleave it into two molecules, and the apparatus may be considered to act as a xe2x80x9cnanotomexe2x80x9d, by analogy with the prior-art microtome which cuts thin sheets of material off of a larger sample.
Thus, in accordance with yet another aspect of the present invention, a method of cleaving at least one substance selected from the group consisting of molecules, molecular complexes, and supramolecular complexes and mixtures thereof is provided, comprising:
providing the nanopore;
placing the nanopore in an ionic solution containing at least one copy of the substance to be cleaved so that a continuous path of the ionic solution through the nanopore is established;
adjusting the width of the nanopore to a desired first width;
establishing an ionic electric current of desired direction and magnitude through the nanopore;
sensing the presence in the nanopore of the substance to be cleaved, the sensing occurring by means of a change in the magnitude of the ionic current; and
decreasing the width of the nanopore to a second width small enough to cleave the substance.
If it is desired to capture a long molecule for purposes of manipulation, the area of the adjustable nanopore may be changed while electrical current monitoring indicates that the molecule is passing through the nanopore. In this event, the apparatus of the present invention captures the molecule, and the apparatus may be considered to act as a xe2x80x9cnanotweezerxe2x80x9d, by analogy with a simple tweezer in which two prongs capture a small part. In contrast to a simple tweezer which, as it captures a part, suddenly localizes it in three dimensions, the nanotweezer serves to first localize the molecule in two dimensions before capturing it to localize it in a third dimension.
Thus, in accordance with a still further aspect of the present invention, a method of capturing at least one substance selected from the group consisting of molecules, molecular complexes, and supramolecular complexes and mixtures thereof is provided, comprising:
providing the nanopore;
placing the nanopore in an ionic solution containing at least one copy of the substance to be captured so that a continuous path of the ionic solution through the nanopore is established;
adjusting the width of the nanopore to a desired first width;
establishing an ionic electric current of desired direction and magnitude through the nanopore;
sensing the presence in the nanopore of the substance to be captured, the sensing occurring by means of a change in the magnitude of the ionic current; and
decreasing the width of the nanopore to a second width small enough to capture the substance and hold it.